Moved @westpasoftware.bsky.social. Highly scalable software for weighted ensemble simulations with any dynamics engine, including MD and systems biology.
Joined January 2019
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WESTPA Software retweeted
The bulk of my thesis work was recently published!
We used 19F NMR and weighted ensemble simulations among other methods to explore hidden dimer states of the HIV-1 capsid protein.
If this sounds interesting to you, see the full paper here:
pnas.org/doi/10.1073/pnas.24…
WESTPA Software retweeted
Just out in @JChemPhys! Integrating Weighted Ensemble (@WestpaSoftware) with OPES-Flooding for accurate and efficient calculation of rare-event kinetics involving barrier crossing and diffusion (e.g. protein folding, ligand binding) @uoCHandBIC #compchem doi.org/10.1063/5.0239303
Check out this recent publication from the @agrossfield lab where they used WESTPA to determine the effects of system size on free energy landscapes of a phase-separating ternary lipid bilayer!
pubs.aip.org/aip/jcp/article…
WESTPA Software retweeted
New work on protein design...
🚨S2 immunogen design using advanced simulation @WestpaSoftware
WE MD--> opening mechanism--> design--> stabilized protein--> cryoEM structure + immunology
@xandra_nuqui @LCasalino88 @McLellan_Lab @ChandranLab
nature.com/articles/s41467-0…
We are excited to share this collaboration between the Gardner and Chong labs in which weighted ensemble simulations are combined with NMR and ensemble docking! jbc.org/article/S0021-9258(2…
WESTPA Software retweeted
#HighlightOfTheWeek Animated time-evolution of a 2D probability distribution obtained using WEDAP, a python package to plot molecular simulation data.
Work by @darianyang and @ltchong.
#compchem
pubs.acs.org/doi/10.1021/acs…
We're excited to see Shirley Ahn's group using WESTPA to explore optimizing weighted ensemble simulations with cumulative distribution functions! pubs.aip.org/aip/jcp/article…
Having trouble visualizing your data from WESTPA?
Try WEDAP! A user-friendly plotting package from @darianyang and @ltchong (1/4)
pubs.acs.org/doi/10.1021/acs…
Want to try it out? Just run: "pip install wedap"
- PyPI: pypi.org/project/wedap/
- GitHub: github.com/darianyang/wedap
- Docs Page: darianyang.github.io/wedap
(4/4)
WESTPA Software retweeted
Thrilled to share that my thesis manuscript is out!
Here, we used WESTPA2 to show that mutations in Abl1 lead to drug resistance by dramatically shifting relative state populations, impacting the conformational search step of binding.
Link below:
biorxiv.org/content/10.1101/…
WESTPA Software retweeted
Revisiting Textbook Azide-Clock Reactions: A “Propeller-Crawling” Mechanism Explains Differences in Rates | Journal of the American Chemical Society @ltchong @PittChem @PittTweet #Azide #Clock #PropellerCrawling #Mechanism #Rates pubs.acs.org/doi/10.1021/jac…
Another great BPS with both vintage and fresh WESTPA developers/users from the @ltchong @RommieAmaro @DMZuckermanLab @Terrasztain and Ahn Labs!
WESTPA Software retweeted
Register now for the free WESTPA Workshop @Pitt_Chemistry, June 20-21. Explore rare event simulations like protein folding, ligand binding, & chemical reactions with our open-source software. Perfect for those using AMBER, NAMD, GROMACS, etc. Reg info:
forms.gle/6gJF6jJ72iexbDTq8
Using WE simulations and experiments, @ChongLabPitt and the Horne lab explore the atomistic folding pathways of protein mimetics
pubs.rsc.org/en/content/arti…
Want to see WE / WESTPA applied towards understanding the free-energy landscape of phase separation in lipid bilayers? Check it out:
This Post is from an account that no longer exists. Learn more
WESTPA Software retweeted
Beyond coarse-grained modeling: Seconds-timescale protein conformational change measured using Cu(II)-based EPR and weighted ensemble MD simulations. @ltchong
Congratulations to Xiaowei and @AnthonyBogetti on this work, now published in Protein Science: onlinelibrary.wiley.com/doi/…
Congrats to one of our core WESTPA developers Jeremy Leung for receiving a MolSSI software fellowship!
We loved having our 2023-24 MolSSI Software Fellows with us last week! We thank Jessica Nash @jessica_a_nash and the other MolSSI Software Scientists for another inspired week of programming and mentorship!
Brossard and Corcelli just published their first paper using WESTPA! They investigated the mechanism for binding a small molecule to the minor groove of DNA.
pubs.acs.org/doi/10.1021/acs…
